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Author Notes:

To whom correspondence should be addressed. Tel: +1 404 727 8491; Fax: +1 404 727 3746; Email: ude.yrome@gnehcx

The authors thank Professor Stephen E. Halford FRS for discussion.

Data for this study were measured at the beamline SERCAT-22 of the Advanced Photon Source at Argonne National Laboratory.

Figures were drawn using the program Pymol, a user-sponsored molecular modeling system with an OPEN-SOURCE foundation (http://pymol.sourceforge.net).

Atomic coordinates have been deposited in the Protein Data Bank with accession numbers 2FKC and 2FKH (pre-reactive complexes), 2FL3 (binary complex) and 2FLC (post-reactive complex).

Conflict of interest statement. None declared.

Subjects:

Research Funding:

The study was partly supported by US Public Health Service grants GM068680 and GM49245 (J.R.H., X.Z., Z.Y. and X.C.) and New England Biolabs (R.J.R., R.M. and G.G.W.)

Financial support for the beamline operation of Emory's shares comes from the Dean's Office of Emory University School of Medicine.

Funding to pay the Open Access publication charges for this article was provided by New England Biolabs.

DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion

Tools:

Journal Title:

Nucleic Acids Research

Volume:

Volume 34, Number 3

Publisher:

, Pages 939-948

Type of Work:

Article | Final Publisher PDF

Abstract:

HinP1I recognizes and cleaves the palindromic tetranucleotide sequence G↓CGC in DNA. We report three structures of HinP1I–DNA complexes: in the presence of Ca2+ (pre-reactive complex), in the absence of metal ion (binary complex) and in the presence of Mg2+ (post-reactive complex). HinP1I forms a back-to-back dimer with two active sites and two DNA duplexes bound on the outer surfaces of the dimer facing away from each other. The 10 bp DNA duplexes undergo protein-induced distortions exhibiting features of A-, B- and Z-conformations: bending on one side (by intercalation of a phenylalanine side chain into the major groove), base flipping on the other side of the recognition site (by expanding the step rise distance of the local base pair to Z-form) and a local A-form conformation between the two central C:G base pairs of the recognition site (by binding of the N-terminal helix in the minor groove). In the pre- and post-reactive complexes, two metals (Ca2+ or Mg2+) are found in the active site. The enzyme appears to cleave DNA sequentially, hydrolyzing first one DNA strand, as seen in the post-reactive complex in the crystalline state, and then the other, as supported by the observation that, in solution, a nicked DNA intermediate accumulates before linearization.

Copyright information:

© The Author 2006. Published by Oxford University Press. All rights reserved. The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

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